It has not actually been determined that ANY pilot made the controll inputs into 587. It has been INFERRED that the pilots made the controll inputs.
There was an incident at AA in the past where an autopilot clutch did not disengage from the rudder axis and submitted the aircraft to extreme yaw motions back and forth including movement of the rudder puddels by the autopilot. The aircraft was landed in Miami with damage. The A/D that resulted from that incident found another aircraft with a similar problem (in a nutshell it was a wire chafing problem)
Cheers
Wino